Vertex component analysis: a geometric-based approach to unmix hyperspectral data

Hyperspectral remote sensing exploits the electromagnetic scattering patterns of the different materials at specific wavelengths [2, 3]. Hyperspectral sensors have been developed to sample the scattered portion of the electromagnetic spectrum extending from the visible region through the near-infrared and mid-infrared, in hundreds of narrow contiguous bands [4, 5]. The number and variety of potential civilian and military applications of hyperspectral remote sensing is enormous [6, 7]. Very often, the resolution cell corresponding to a single pixel in an image contains several substances (endmembers) [4]. In this situation, the scattered energy is a mixing of the endmember spectra. A challenging task underlying many hyperspectral imagery applications is then decomposing a mixed pixel into a collection of reflectance spectra, called endmember signatures, and the corresponding abundance fractions [8–10]. Depending on the mixing scales at each pixel, the observed mixture is either linear or nonlinear [11, 12]. Linear mixing model holds approximately when the mixing scale is macroscopic [13] and there is negligible interaction among distinct endmembers [3, 14]. If, however, the mixing scale is microscopic (or intimate mixtures) [15, 16] and the incident solar radiation is scattered by the scene through multiple bounces involving several endmembers [17], the linear model is no longer accurate. Linear spectral unmixing has been intensively researched in the last years [9, 10, 12, 18–21]. It considers that a mixed pixel is a linear combination of endmember signatures weighted by the correspondent abundance fractions. Under this model, and assuming that the number of substances and their reflectance spectra are known, hyperspectral unmixing is a linear problem for which many solutions have been proposed (e.g., maximum likelihood estimation [8], spectral signature matching [22], spectral angle mapper [23], subspace projection methods [24,25], and constrained least squares [26]). In most cases, the number of substances and their reflectances are not known and, then, hyperspectral unmixing falls into the class of blind source separation problems [27]. Independent component analysis (ICA) has recently been proposed as a tool to blindly unmix hyperspectral data [28–31]. ICA is based on the assumption of mutually independent sources (abundance fractions), which is not the case of hyperspectral data, since the sum of abundance fractions is constant, implying statistical dependence among them. This dependence compromises ICA applicability to hyperspectral images as shown in Refs. [21, 32]. In fact, ICA finds the endmember signatures by multiplying the spectral vectors with an unmixing matrix, which minimizes the mutual information among sources. If sources are independent, ICA provides the correct unmixing, since the minimum of the mutual information is obtained only when sources are independent. This is no longer true for dependent abundance fractions. Nevertheless, some endmembers may be approximately unmixed. These aspects are addressed in Ref. [33]. Under the linear mixing model, the observations from a scene are in a simplex whose vertices correspond to the endmembers. Several approaches [34–36] have exploited this geometric feature of hyperspectral mixtures [35]. Minimum volume transform (MVT) algorithm [36] determines the simplex of minimum volume containing the data. The method presented in Ref. [37] is also of MVT type but, by introducing the notion of bundles, it takes into account the endmember variability usually present in hyperspectral mixtures. The MVT type approaches are complex from the computational point of view. Usually, these algorithms find in the first place the convex hull defined by the observed data and then fit a minimum volume simplex to it. For example, the gift wrapping algorithm [38] computes the convex hull of n data points in a d-dimensional space with a computational complexity of O(nbd=2cþ1), where bxc is the highest integer lower or equal than x and n is the number of samples. The complexity of the method presented in Ref. [37] is even higher, since the temperature of the simulated annealing algorithm used shall follow a log( ) law [39] to assure convergence (in probability) to the desired solution. Aiming at a lower computational complexity, some algorithms such as the pixel purity index (PPI) [35] and the N-FINDR [40] still find the minimum volume simplex containing the data cloud, but they assume the presence of at least one pure pixel of each endmember in the data. This is a strong requisite that may not hold in some data sets. In any case, these algorithms find the set of most pure pixels in the data. PPI algorithm uses the minimum noise fraction (MNF) [41] as a preprocessing step to reduce dimensionality and to improve the signal-to-noise ratio (SNR). The algorithm then projects every spectral vector onto skewers (large number of random vectors) [35, 42,43]. The points corresponding to extremes, for each skewer direction, are stored. A cumulative account records the number of times each pixel (i.e., a given spectral vector) is found to be an extreme. The pixels with the highest scores are the purest ones. N-FINDR algorithm [40] is based on the fact that in p spectral dimensions, the p-volume defined by a simplex formed by the purest pixels is larger than any other volume defined by any other combination of pixels. This algorithm finds the set of pixels defining the largest volume by inflating a simplex inside the data. ORA SIS [44, 45] is a hyperspectral framework developed by the U.S. Naval Research Laboratory consisting of several algorithms organized in six modules: exemplar selector, adaptative learner, demixer, knowledge base or spectral library, and spatial postrocessor. The first step consists in flat-fielding the spectra. Next, the exemplar selection module is used to select spectral vectors that best represent the smaller convex cone containing the data. The other pixels are rejected when the spectral angle distance (SAD) is less than a given thresh old. The procedure finds the basis for a subspace of a lower dimension using a modified Gram–Schmidt orthogonalizati on. The selected vectors are then projected onto this subspace and a simplex is found by an MV T pro cess. ORA SIS is oriented to real-time target detection from uncrewed air vehicles using hyperspectral data [46]. In this chapter we develop a new algorithm to unmix linear mixtures of endmember spectra. First, the algorithm determines the number of endmembers and the signal subspace using a newly developed concept [47, 48]. Second, the algorithm extracts the most pure pixels present in the data. Unlike other methods, this algorithm is completely automatic and unsupervised. To estimate the number of endmembers and the signal subspace in hyperspectral linear mixtures, the proposed scheme begins by estimating sign al and noise correlation matrices. The latter is based on multiple regression theory. The signal subspace is then identified by selectin g the set of signal eigenvalue s that best represents the data, in the least-square sense [48,49 ], we note, however, that VCA works with projected and with unprojected data. The extraction of the end members exploits two facts: (1) the endmembers are the vertices of a simplex and (2) the affine transformation of a simplex is also a simplex. As PPI and N-FIND R algorithms, VCA also assumes the presence of pure pixels in the data. The algorithm iteratively projects data on to a direction orthogonal to the subspace spanned by the endmembers already determined. The new end member signature corresponds to the extreme of the projection. The algorithm iterates until all end members are exhausted. VCA performs much better than PPI and better than or comparable to N-FI NDR; yet it has a computational complexity between on e and two orders of magnitude lower than N-FINDR. The chapter is structure d as follows. Section 19.2 describes the fundamentals of the proposed method. Section 19.3 and Section 19.4 evaluate the proposed algorithm using simulated and real data, respectively. Section 19.5 presents some concluding remarks.

Downstream processing development of enveloped viruses for clinical applications: innovative tools for rational process optimization

Dissertation presented to obtain a Ph.D. degree in Engineering and Technology Sciences, Biotechnology at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

O papel dos sistemas de Non-Intrusive Load Monitoring para a eficiência energética do setor residencial

A sustentabilidade energética do planeta é uma preocupação corrente e, neste sentido, a eficiência energética afigura-se como sendo essencial para a redução do consumo em todos os setores de atividade. No que diz respeito ao setor residencial, o indevido comportamento dos utilizadores aliado ao desconhecimento do consumo dos diversos aparelhos, são factores impeditivos para a redução do consumo energético. Uma ferramenta importante, neste sentido, é a monitorização de consumos nomeadamente a monitorização não intrusiva, que apresenta vantagens económicas relativamente à monitorização intrusiva, embora levante alguns desafios na desagregação de cargas. Abordou-se então, neste documento, a temática da monitorização não intrusiva onde se desenvolveu uma ferramenta de desagregação de cargas residenciais, sobretudo de aparelhos que apresentavam elevados consumos. Para isso, monitorizaram-se os consumos agregados de energia elétrica, água e gás de seis habitações do município de Vila Nova de Gaia. Através da incorporação dos vetores de água e gás, a acrescentar ao da energia elétrica, provou-se que a performance do algoritmo de desagregação de aparelhos poderá aumentar, no caso de aparelhos que utilizem simultaneamente energia elétrica e água ou energia elétrica e gás. A eficiência energética é também parte constituinte deste trabalho e, para tal, implementaram-se medidas de eficiência energética para uma das habitações em estudo, de forma a concluir as que exibiam maior potencial de poupança, assim como rápidos períodos de retorno de investimento. De um modo geral, os objetivos propostos foram alcançados e espera-se que num futuro próximo, a monitorização de consumos não intrusiva se apresente como uma solução de referência no que respeita à sustentabilidade energética do setor residencial.

Chagas' disease in the Brazilian Amazon: II. A serological survey

A serological survey, involving indirect immunofluorescence testing of blood sera samples, was carried out on the residents of one in every five dwellings in the town of Barcelos (in the northern part of the State of Amazonas, on the right bank of the Rio Negro, 490 Km from Manaus by river) and on the rural populations of the villages of Piloto and Marará (also on the right bank of the Rio Negro, 30 minutes by boat from Barcelos). A total of 710 sera samples were tested, 628 from the resident population in the town of Barcelos, 35 from Piloto and 47 from Marará. The tests were carried out using human anti-gammaglobulin type IgG (Biolab) and antigen from formolized culture of T.cruzi Y strain. The sera were serially diluted from 1:40 to 1:320 in PBS 7.2. Of the 710 samples examined 89(12.5%) were positive for anti-T.cruzi antibodies: 2 of these (2.2%) at a dilution of 1:320; 12(13.4%) at 1:160; 38 (42.6%) at 1:80; and the remainder at 1:40, giving a median serological dilution of 1:80. The following questions are discussed: the high serological prevalence for Chagas'infection found in our survey; the possibility of serological cross-reactions; the need for confirmatory tests for the positives reactions; and the strong correlation between our results and preliminary epidemiological data (such as the level of human contact with wild triatominae, know locally as "Piacava's lice". We draw attention to the isolation by xenodiagnosis of one strain of T.cruzi from a patient with positive serology for Chagas' infection.

Bancroftian filariasis in two urban areas of Recife, Brasil: the role of individual risk factors

Bancroftian filariasis is spreading in towns of endemic areas as in Recife, northeastern Brazil, where it is a major public health problem. This paper deals with the prevalence of microfilaraemia and filarial disease in two urban areas of Recife, studying their association with individual characteristics and variables related to the exposure to the vectors. The parasitologic survey was performed through a "door-to-door" census and microfilaraemia was examined by the thick-drop technique using 45µl of peripheral blood collected between 20:00 and 24:00 o' clock. 2,863 individuals aged between 5 and 65 years were interviewed and submitted to clinical examination. Males aged between 15 and 44 years old presented the greatest risk of being microfilaraemic. Microfilaraemia was also significantly associated with no use of bednet to sleep. The risk of being microfilaraemic was greater among those who had lived in the studied areas for more than 5 years. The overall disease prevalence was 6.3%. Males presented the greatest risk of developing acute disease. The risk of developing chronic manifestations was also greater among males and increased with age. We found no association between time of residence, bednet use, microfilaraemia and acute and chronic disease. We may conclude that in endemic areas there are subgroups of individuals who has a higher risk of being microfilariae carriers due to different behaviours in relation to vector contact.

Trypanosoma cruzi strains: behavior after passage into authoctonous or foreign species of triatomine (biological and biochemical patterns)

The behavior of T. cruzi strains from S. Felipe - BA (19 SF, 21 SF and 22 SF) classified as Type II Zymodeme 2, was investigated after passage through the authoctonous (P. megistus) and foreign vectors (T. infestans and R. prolixus). For each strain Swiss mice were infected: I - with blood forms (control); II - with metacyclic forms (MF) from P. megistus; III - with MF from T. infestans; IV - with MF from R. prolixus. Inocula: MF from the three species of triatomine, 60 to 120 days after feeding in infected mice, adjusted to 10 4. Biological behavior in mice (parasitemia, morphology, mortality, virulence and pathogenicity) after passage through triatomine was compared with data from the same strain in control mice. Isoenzymic electrophoresis (ASAT, ALAT, PGM, GPI) were also performed after culture into Warren medium. The three strains maintained the isoenzyme profiles (zymodeme 2), in the control groups and after passages through different species of triatomine. Biological characterization disclosed Type II strains patterns for all groups. An increased virulence was observed with the 22 SF strain isolated from P. megistus and T. infestans and higher levels of parasitemia and predominance of slender forms in mice inoculated with the 19 SF and 21 SF from these same species. Results indicate that the passage through the two species T. infestans and P. megistus had a positive influence on the virulence of the regional strains of S. Felipe, regardless of being autocthonous (P. megistus) or foreign to the area (T. infestans).

Traços da medicina na azulejaria de Lisboa

RESUMO: A presente abordagem procura estabelecer uma relação entre a Medicina e a Azulejaria. Um conjunto de composições produzidas entre o século XVII e a década de 90 do século XX, localizado na área de Lisboa e seus arredores, organiza-se em torno de oito vectores que ilustram a presença de alusões à Medicina na Azulejaria da referida área. São estes, aspectos relacionados com a higiene, marcos da história da assistência, ciclos temáticos relacionados com os quatro elementos primordiais e com os cinco sentidos, representações ligadas à ideia de morte, episódios bíblicos, referências hagiográficas e elementos ligados à acção médica, como objectos, patologias, instituições ou acontecimentos, associados à Medicina, que atestam esta relação entre Arte e Ciência, de forma geral, e entre a Azulejaria e a Medicina, de forma particular. À análise destes vectores, antecede uma resenha histórica relativa à ligação entre Arte e Ciência e um apontamento histórico acerca da história da Azulejaria. Pretende-se demonstrar esta conexão interdisciplinar e reforçar a importância da vertente humanista da Medicina, na sua história, na sua aprendizagem e na sua prática.-------------------------------------ABSTRACT: The present approach aims at establishing a relation between Medicine and Tile Art. A group of compositions produced between the 17th century and the 1990s, located in the Lisbon area and its surroundings, is organized around eight vectors that illustrate the presence of allusions to Medicine in the Tile Art in the mentioned areas. These are related with hygiene aspects, landmarks in the history of assistance, thematic cycles related with the four main elements and with the five senses, representations connected to the idea of death, biblical episodes, hagiographic references and elements connected to the medical intervention, such as objects, pathologies, institutions or events related to Medicine that testify this relation between Art and Science in a broad context, and between Tile Art and Medicine in a strict sense. Prior to the analysis of these vectors there is a historic contextualization concerning the relationship between Art and Science and a historical note about the history of Tile Art. The aim is to demonstrate the interdisciplinary relation and reinforce the importance of the humanistic side of Medicine, in its history, its learning and its practice.------------------------------------RÉSUMÉ: Cet étude vise établir une relation entre la Médecine et l’Art de l’ « Azulejaria ». Un ensemble de compositions produites entre le XVII ème siècle et le dernier quart du XX ème siècle, dans la région de Lisbonne, s’organise autour de huit axes qui illustrent des références à la médecine. Nous avons récupéré des motifs allusifs à l’hygiène, à l’histoire de l’assistance, aux cycles thématiques des quatre éléments primordiaux et des cinq sens, à la mort, aux épisodes bibliques ou hagiographiques mais aussi aux motifs qui reproduisent des objets, des pathologies, des institutions ou des évènements médicaux. Tous ces exemples mettent à jour la relation entre l’Art et la Science, en général, et entre l’ « Azulejaria» et la Médecine, en particulier. Avant d’analyser ces huit axes, nous établirons un parcours historique pour expliquer la relation entre Art et Science, ainsi qu’une brève histoire de l’ «azulejaria». Nous prétendons démontrer cette relation interdisciplinaire et renforcer l’importance de la vertu humaniste des Sciences Médicales dans son histoire, son apprentissage et sa pratique.

Seropositivity for anti-Trypanosoma cruzi antibodies among blood donors of the "Hospital Universitário Regional do Norte do Paraná", Londrina, Brazil

The most frequent form of acquisition of Chagas' disease in endemic areas was the transmission through the feces of contaminated triatominae. However, special attention should be paid in urban areas to transmission by blood transfusion, justifying the compulsory screening of blood donors. Early investigations at blood banks in the town of Londrina, Brazil, demonstrated that the seroprevalence of anti-Trypanosoma cruzi antibodies among blood donors was approximately 7.0% in the fifties9,34. Further studies demonstrated pratically the same seroprevalence until the eighties4,32,41. In an attempt to obtain data about the real dimension of the seropositivity for anti-Trypasonoma cruzi antibodies in the region, the authors carried out a large-scale study on 45,774 serum samples from blood donors of the Hemocentro of Hospital Universitário Regional do Norte do Paraná (HURNP), Universidade Estadual de Londrina. The immunological tests were done at the Division of Clinical Immunology of HURNP from May 1990 to December 1994. The serum samples were studied by the indirect hemagglutination assay (IHA, using kits commercially obtained from EBRAM) and by indirect immunofluorescence (IFI, using kits from LIO SERUM) with anti-human IgG conjugate (LABORCLIN). The results demonstrated that 643 serum samples were positive in both assay corresponding to a seroprevalence of 1.4%, i.e., a significant decrease in anti-Trypanosoma cruzi antibodies in the region in comparison with the previously mentioned rates. Data correlating sex and age of seropositive blood donors are presented, as well as the possible factors that may have contributed to the results observed.

A Leishmaniose visceral em Portugal Continental : 1999-2009

RESUMO - As alterações climáticas alteraram a incidência e distribuição mundial de zoonoses, ao modificarem o perfil epidemiológico dos seus vectores. A leishmaniose visceral é reemergente na bacia mediterrânica, sendo o seu impacto real subestimado. Em Portugal, é endémica em três regiões, de declaração obrigatória desde 1948 e o reservatório é o canídeo. O aumento da incidência da doença no cão e a escassez de informação epidemiológica tornou pertinente investigar a realidade nacional. A partir das bases de dados das notificações e dos grupos de diagnósticos homogéneos hospitalares, foram identificados todos os casos e, consultados todos os processos clínicos dos doentes com episódios de internamento nos hospitais do continente entre 1999-2009. Ocorreram 730 internamentos para 375 indivíduos na maioria: homens, eurocaucasianos, com em média, 27 anos e, residência em Lisboa e Vale do Tejo. A sintomatologia e comorbilidades dos doentes vão de encontro ao descrito internacionalmente. A doença foi subnotificada, com uma demora média de 19 dias. A letalidade foi de 5%. A taxa de incidência média do continente foi de 0,294/100000 habitantes, sem padrão de sazonalidade. O corredor endémico de Bortman construído apresentou picos com amplitudes de 2-3 anos. O mapeamento dos doentes evidenciou casos em regiões não endémicas acompanhando a distribuição da leishmaniose canina. Seria pertinente que futuras investigações construíssem uma modelação matemática que confirmasse a tendência do corredor endémico (pico em 2011?) para accionar um sistema de alerta nos Serviços de Saúde. Seria também útil a avaliação das condições geoclimáticas das localidades com casos para evidenciar possíveis similitudes no território. -------ABSTRACT - Climate changed the incidence and worldwide distribution of zoonosis while the epidemiological profile of their vectors was changing. Visceral leishmaniasis is reemerging in the Mediterranean basin and its real impact underestimated. In Portugal, it’s endemic in three regions; the notification occurs since 1948 and dog is the reservoir. The increased incidence of the canines’ disease and the scarcity of epidemiological information relevant investigate the national reality. From Notifications and Homogeneous’ Diagnostics Groups system databases, all cases were identified and also analyze all clinical processes of inpatients’ hospitals in 1999- 2009 in Portugal. 730 admissions occurred for 375 patients. In most they were men, Caucasians, with an average of 27 years and residency in Lisboa e Vale do Tejo. The symptoms and comorbilidades patient go against described internationally. The disease was under notified, with an average delay of 19 days. Lethality was 5%. The incidence rate was 0,294/100000 inhabitants, without seasonality. The endemic’s Bortman corridor presents peak amplitudes of 2-3 years. Mapping patient’s residency shows that cases’ distribution is similar to endemic canine leishmaniasis. It would be appropriate a research to build a mathematical modeling up to confirm the trend of corridor endemic (peak in 2011?), to trigger an alert system for health services. It would also be useful to evaluate the geo-climatics conditions of localities with cases to highlight possible similarities in the territory.

Expression of antibodies and retroviralVectors from defined chromosomal sites: strategies towards reliable production systems

Dissertation presented to obtain a Ph.D. degree in Sciences of Engineering and Technology, Cell Technology, at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

COLONIZATION AND LABORATORY MAINTENANCE OFAnopheles albimanus WIEDEMANN IN VENEZUELA

Anopheles albimanus is one of the main vectors of malaria in Central America and the Caribbean, based on its importance, there are previous reports of the successful colonization of this species in Latin America countries. Mosquitoes were collected in the Aragua State of Venezuela colonized in the laboratory, using a simple and efficient maintenance method. Based on life table calculations under well established laboratory conditions, the Survival Rate Probability was constant and always close to 1 in immature stages, the Reproductive Net Rate (Ro) was 3.83, the generation time (Tc) was 24.5 days and the Intrinsic Growth Rate (rm) was 0.0558. This is the first report of the colonization of A. albimanus in Venezuela.

Cavin 1 and cavin 2 roles on adipocyte cell function

Dissertação para obtenção do Grau de Mestre em Genética Molecular e Biomedicina

Oral transmission of Chagas disease: importance of Trypanosoma cruzi biodeme in the intragastric experimental infection

Oral transmission of Trypanosoma cruzi has been suspected when epidemic episodes of acute infection were observed in areas devoid of domiciled insect vectors. Considering that the distribution of T. cruzi biodemes differs in sylvatic and domestic cycles, results of studies on biodemes can be of interest regarding oral transmission. The infectivity of T. cruzi strains of different biodemes was tested in mice subjected to infection by the digestive route (gavage). Swiss mice were infected either with the Peruvian strain (Biodeme Type I, Z2b) or the Colombian strain (Biodeme Type III, Z1, or T. cruzi I); for control, intraperitoneal inoculation was performed in a group of mice. The Colombian strain revealed a similar high infectivity and pathogenicity when either route of infection was used. However, the Peruvian strain showed contrasting levels of infectivity and pathogenicity, being high by intraperitoneal inoculation and low when the gastric route was used. The higher infectivity of the Colombian strain (Biodeme Type III) by gastric inoculation is in keeping with its role in the epidemic episodes of acute Chagas disease registered in the literature, since strains belonging to Biodeme III are most often found in sylvatic hosts.

Evidence of spotted fever group rickettsiae in state of Rio de Janeiro, Brazil

Ticks were obtained from dogs from February to September of 1999 at weekly intervals, in the County of Piraí, State of Rio de Janeiro. Four hundred seventy four ixodids were taxonomically identified, 103 Amblyomma cajennense, seven Amblyomma ovale, 209 Rhipicephalus sanguineus, and 155 Amblyomma sp. An hemolymph test associated with Giemsa's stain revealed two specimens in 163 ticks tested (R. sanguineus and Amblyomma sp), containing rickettsia-like organisms. Direct immunofluorescence verified the presence of spotted fever group rickettsia in one specimen of R. sanguineus. Considering the limited information on rickettsiosis in Brazil, principally in relation to the vectors involved in perpetuating it in foci, these preliminary results give us an idea on the importance of infection in ticks, allowing to expand our knowledge on this zoonosis.

Assessment of PCR in the detection of Leishmania spp in experimentally infected individual phlebotomine sandflies (Diptera: Psychodidae: Phlebotominae)

DNA amplification by the polymerase chain reaction (PCR) was applied in the investigation of the presence of Leishmania (Kinetoplastida: Trypanosomatidae) parasites in single phlebotomine sandflies. Three phlebotomine/parasite pairs were used: Lutzomyia longipalpis/Leishmania chagasi, Lutzomyia migonei/Leishmania amazonensis and Lutzomyia migonei/Leishmania braziliensis, all of them incriminated in the transmission of visceral or cutaneous leishmaniasis. DNA extraction was performed with whole insects, with no need of previous digestive tract dissection or pooling specimens. The presence of either mouse blood in the digestive tract of the sandflies or the digestive tract itself did not interfere in the PCR. Infection by as few as 10 Leishmania sp. per individual were sufficient for DNA amplification with genus-specific primers. Using primers for L. braziliensis and L. mexicana complexes, respectively, it was possible to discriminate between L. braziliensis and L. amazonensis in experimentally infected vectors (L. migonei).